def parse_pato(ontology_file):
terms = []
for elt in parseGOOBO(ontology_file):
terms.append(elt["name"])
if 'synonym' in elt:
if isinstance(elt['synonym'], list):
for syn in elt['synonym']:
try:
terms.append(syn.split('"')[1])
except:
print 'error parsing ontology synonym'
else:
try:
terms.append(elt['synonym'].split('"')[1])
except:
print 'error parsing ontology synonym non list'
blacklist = read_blacklist()
blacklist.extend([stem(b) for b in blacklist])
#blacklist = [stem_word(b) for b in blacklist]
return [
pheno.lower() for pheno in terms
if pheno.lower() not in blacklist and len(pheno) > 1
]
return terms
def parse_pato(ontology_file):
terms = []
for elt in parseGOOBO(ontology_file):
#terms.append(elt["name"])
#if len(elt["name"].split()) > 1:
p = re.sub(r'\([^)]*\)', ' ', elt["name"])
terms.extend(p.split())
if 'synonym' in elt:
if isinstance(elt['synonym'], list):
for syn in elt['synonym']:
try:
#terms.append(syn.split('"')[1])
#if len(syn.split('"')[1].split()) > 1:
p = re.sub(r'\([^)]*\)', ' ', syn.split('"')[1])
terms.extend(p.split())
except:
print 'error parsing ontology synonym'
else:
try:
#terms.append(elt['synonym'].split('"')[1])
#if len(elt['synonym'].split('"')[1].split()) > 1:
p = re.sub(r'\([^)]*\)', ' ', elt['synonym'].split('"')[1])
terms.extend(p.split())
except:
print 'error parsing ontology synonym non list'
terms = list(set(terms))
blacklist = read_blacklist()
return [
pheno.lower() for pheno in terms if pheno.lower() not in blacklist
and len(pheno) > 1 and re.search(r'[a-zA-Z]', pheno)
]
def parse_ontology(ontology_file):
terms = []
for elt in parseGOOBO(ontology_file):
#terms.append(elt["name"])
#if len(elt["name"].split()) > 1:
p = re.sub(r'\([^)]*\)', ' ', elt["name"])
terms.extend(p.split())
if 'synonym' in elt:
if isinstance(elt['synonym'], list):
for syn in elt['synonym']:
try:
#terms.append(syn.split('"')[1])
#if len(syn.split('"')[1].split()) > 1:
p = re.sub(r'\([^)]*\)', ' ', syn.split('"')[1])
terms.extend(p.split())
except:
print 'error parsing ontology synonym'
else:
try:
#terms.append(elt['synonym'].split('"')[1])
#if len(elt['synonym'].split('"')[1].split()) > 1:
p = re.sub(r'\([^)]*\)', ' ', elt['synonym'].split('"')[1])
terms.extend(p.split())
except:
print 'error parsing ontology synonym non list'
terms = list(set(terms))
return terms
def parse_pato(ontology_file):
terms = []
for elt in parseGOOBO(ontology_file):
terms.append(elt["name"])
if 'synonym' in elt:
if isinstance(elt['synonym'], list):
for syn in elt['synonym']:
try:
terms.append(syn.split('"')[1])
except:
print 'error parsing ontology synonym'
else:
try:
terms.append(elt['synonym'].split('"')[1])
except:
print 'error parsing ontology synonym non list'
return terms
"""
Output fields:
id, name, synonyms, related terms, alt IDs, parent, MeSh terms
"""
import argparse
from obo_parser import parseGOOBO
if __name__ == "__main__":
parser = argparse.ArgumentParser()
parser.add_argument('infile', help='Input HPO file in OBO v1.2 format.')
parser.add_argument('outfile', help='Output TSV file name.')
args = parser.parse_args()
with open(args.outfile, 'w') as out:
for term in parseGOOBO(args.infile):
id = term['id'][0]
name = term['name'][0]
alt_ids = '|'.join(term['alt_id']) if 'alt_id' in term else ''
is_a = '|'.join(x.partition(' ')[0]
for x in term['is_a']) if 'is_a' in term else ''
synonyms = set()
related = set()
mesh = set()
for s in term.get('synonym', []):
if ' EXACT [' in s:
synonyms.add(s.split(' EXACT [')[0].strip('" '))
else:
# RELATED, BROAD, etc.
related.add(s.split('" ')[0].strip('"'))
for n in term.get('xref', []):
import argparse
from obo_parser import parseGOOBO
if __name__ == "__main__":
parser = argparse.ArgumentParser()
parser.add_argument('infile', help='Input HPO file in OBO v1.2 format.')
parser.add_argument('outfile', help='Output TSV file name.')
args = parser.parse_args()
with open(args.outfile, 'w') as out:
for term in parseGOOBO(args.infile):
id = term['id'][0]
name = term['name'][0]
alt_ids = '|'.join(term['alt_id']) if 'alt_id' in term else ''
is_a = '|'.join(x.partition(' ')[0] for x in term['is_a']) if 'is_a' in term else ''
synonyms = set()
related = set()
for s in term.get('synonym', []):
if ' EXACT [' in s:
synonyms.add(s.split(' EXACT [')[0].strip('" '))
else:
# RELATED, BROAD, etc.
related.add(s.split('" ')[0].strip('"'))
for n in term.get('xref', []):
if ' ' in n:
synonyms.add(n.partition(' ')[-1].strip('" '))
synonyms.discard(name)
related.discard(name)
synonyms = '|'.join(sorted(synonyms)) if synonyms else ''